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From: fischl@nmr.mgh.harvard.edu
Date: Fri, 8 Apr 2016 09:56:46 -0400
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] errors on the WM and Gray inflated surfaces

Dear FS expert and users,

We are coming across errors on the WM and Gray inflated surfaces.

When trying to open the surfaces with tksurfer as follows (tksurfer subid lh inflated -gray) 

We get only a small part of the cortex displaying.  

 

<Screenshot.jpg>

 

 

<Screenshot-1.jpg>

 

Also when we try file-label-import annotation  the following error occurs:

colortable with 13 entries read (originally /usr/local/apps/freesurfer/5.1.0/average/colortable_BA.txt)

Found embedded color table in annotation.

There seem to be no hard failures as recon-all log said "finished without errors". Also WM and pial surfaces look accurate.

Now we are trying to figure what is that could have caused this for all subjects.

We have an old instructions for freesurfer saying to to run recon-all as follows.

run recon -all -s subjID /autorecon -all 

As I am not familiar with this way of running recon-all I wanted to ask if this could have caused the problem consistently across 70~ subjects.

Any advise on this would be greatly appreciated.

Cheers.

Pablo

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